Just a quick blog post this week on some new plant science podcasts, for your entertainment!
First, Radio 4’s much-retweeted Plants: From Roots to Riches. This programme has been running all month and ends today so it’s not really news, but I’ve been listening to this bit by bit and was delighted to hear a familiar voice in the ‘Signals of Growth‘ episode. Nick Harberd, one of our Advisory Committee members, discussed the Green Revolution wheat and rice varieties with presenter Kathy Willis.
This is a great series, although the episodes are quite short and only focus on a small area of plant science so I’d advise skipping any episodes on a topic you know too much about or that just isn’t of interest to you. Highlights for me so far have been the ‘Blight on the Landscape‘ episode about plant-microbe interactions, which had a very interesting section on Beatrix Potter’s work on lichens; and the episode based entirely around Kew’s Arboretum, ‘An Ill Wind‘, which gave me a new appreciation of the great value of tree science and forestry.
Friday’s episode was about Arabidopsis – I haven’t reached that one yet though!
Second, videos of talks from the UK Plant Sciences Federation conference PlantSci 2014 are now available on the Journal of Experimental Botany YouTube channel. The talks were all excellent and the videos make good teaching resources. All the speakers pitched their science for a well-informed general audience, and all were clear about why their research is important. The highlight of the conference for me was the panel discussion about UK plant science challenges, achievements and future needs and I’m happy to see that it’s there in it’s entirety, including the comments from the floor – all 1 hour 27 minutes of it.
It’s been very quiet here on the blog recently, but we’re pretty much caught up after being away at the International Conference on Arabidopsis Research in Vancouver (you can still see the #ICAR2014 stream here). Things will be back to normal very soon.
Proving that science and art aren’t mutually exclusive, check out this gorgeous animation that has recently been produced by engineer-turned-Fine Art student Andrew Styan.
this much is known from Andrew Styan on Vimeo.
Andrew recently took part in a science-art course, tutored in part by Dr Gordon Simpson, an Arabidopsis researcher who works within Dundee’s Department of Plant Sciences.
Inspired by Dr Simpson’s work, Andrew’s animation This Much is Known represents 25 years of Arabidopsis research and demonstrates how our understanding of this little weed has expanded in such a relatively short time.
Using the Scopus database, he searched for all Arabidopsis papers published in the last 25 years, and the keywords associated with them. Each bubble that appears on the screen represents a different keyword, with the size of the bubble growing as more papers on that topic are published.
I think it’s very clever and very beautiful! Thanks Andrew, and Gordon!
If there are any other budding science-artists out there who have produced some cool work on Arabidopsis or other plant science, we’d love to see it so please email firstname.lastname@example.org.
Image by Centimedia.org for GARNet
We have some GARNet news to share!
First of all, we are pleased to finally open registration for the hands-on iPlant training workshop ‘Data Mining with iPlant‘. Unfortunately we’ve had to change the planned location, and it will now be at the University of Warwick. The date is still 17-20 September 2013.
For those who don’t know, iPlant is an incredible free resource which allows its users to access high performance computing power, large scale data storage, and analytical software needed for a variety of data- or compute- intensive research applications.
You can either come for just one day for a free hands-on introduction to iPlant, or stay for four days and get in depth training on how to analyse real data in iPlant. For more information go to: http://www.garnetcommunity.org.uk/news/13-06-19/data-mining-iplant-17-20-september-2013
Our second announcement is more of a save-the-date than an invitation. The GARNet general conference will return next year, possibly for one time only. GARNet 2014: The Past, Present and Future of the Genetic Model Revolution will be held at the University of Bristol on 9-10 September 2014. It will be a celebration of exciting new plant science, and a look at the evolving nature of model systems as well as the brilliant achievements made with them in the past.
The Journal of Experimental Botany kindly recorded and uploaded talks from the last GARNet conference in 2011. Here is Katherine Denby of the University of Warwick talking about the PRESTA project, which since this talk has produced two Plant Cell papers (1,2). You can see the rest of the talks from GARNet 2011 on the JXB website.
To whet your appetite for next week’s UK PlantSci 2013 conference in Dundee, here are clips of the keynote speakers Charles Godfray (University of Oxford) and David Baulcombe (University of Cambridge). I think that the Godfray clip can be considered a very unofficial ‘preview’ of his keynote lecture Feeding 10 Billion People on a Finite Planet, which will be on Tuesday morning. David Baulcombe’s interview probably isn’t linked to his Of maize and men or peas and people lecture on Wednesday morning, but it is still a good watch – an interesting and balanced discussion about GM.
If you’re not coming up to Dundee, you can still keep up with these talks and all the others live on the Twitter hashtag #PlantSci2013. I’ll post the blog posts and reports about the conference here once they’ve trickled out, too.
Video credits: The Oxford Martin School and LEAF
Geraint Parry of the University of Liverpool stepped up to the challenge of communicating the real science of GM at Ignite Liverpool in February. Ignite is a grassroots movement started in Seattle but now established in many cities all over the world. Ignite events consist of many 5-minute powerpoint presentations given by anyone who wants to contribute one about anything they want to talk about. Such a fast-moving event with a diverse audience is of course a great place to communicate science, and you can see Geraint’s excellent presentation in the video above.
If you want to have a go yourself, Ignite Liverpool is next on in May, and there is also an Ignite London, although I don’t know if they will be running another event.
The video is from the Ignite Liverpool YouTube Channel, where you can see other presentations from the event, including this one on ATP.
One of the most frustrating things in lab-based research is trying to learn a new method from a paper. In my short time in the lab, I sometimes had to follow a trail of breadcrumbs back through several papers to find details of a single step in a protocol, on one occasion digging around in the library archives for a paper from an out-of-publication journal. Once the various reagents had been rounded up, I’d interpreted the protocol (What kind of ‘mixing’? How slowly is ‘slowly add’?), and had failed to accurately measure a solution that dissolved my pipette tips, all I usually had to show for my pains was a questionable precipitate and a lot of washing up – at least for the first attempt.
Researchers from three Australian research centres had similar problems with hydroponic systems described in the literature. Conn et al. designed their own hydroponic system for Arabidopsis and published it in Plant Methods (2013, 9:4) along with the YouTube video above, demonstrating exactly how the protocol works in practice. Plant Methods is a friendly journal for the intrepid researcher attempting protocols new to their research group. This paper is typical and has a comprehensive list of necessary reagents and equipment, and clear step-by-step guide with critical points highlighted.
If you need to grow Arabidopsis in a controlled environment to look at the physiology of the whole plant and you are unhappy with your current growth facilities, take a look at this paper on DIY hydroponics. It is quite a work intensive set-up (drill-bits are mentioned) but most of the equipment is cheap and easily come by.
Video Credit: Matthew Gilliham, via YouTube.
The phrase ‘synthetic biology’ doesn’t naturally pair with ‘plant science’ for most plant researchers. Yet at the Biosciences KTN Annual Conference 2012, Impact through the Biosciences, of five talks on synthetic biology, one was an introduction, one was about photosynthesis, and one was about synthesising high value plant compounds in microalgae. You can view all the videos from the meeting here if you are a member of connect_, which is free to join.
Expertise in molecular pathways, plant hormones, bioinformatics, and modelling, could all be applied to synthetic biology. It’s true that currently most synthetic biology, even the plant synthetic biology in the two videos highlighted above, is done in microorganisms or inorganic systems, but plants are the obvious choice for a multi-cellular synthetic biology system.
If you want to find out more about the synthetic biology approach, current plant synthetic biology projects, and the range of synthetic biology tools and resources available, come to our meeting An Introduction to Opportunities in Plant Synthetic Biology. It is an introduction to synthetic biology to plant scientists, and we hope it will encourage the UK plant science community to benefit from the emphasis the government, BBSRC, EPSRC and TSB are placing on synthetic biology.
Video credit: Biosciences KTN, via their YouTube channel.
This video is an introduction to a series of filmed talks from the Forestry Commission Plant Health Conference. It introduces the ash dieback problem nicely and places it in a wider context. A number of experts give their opinions on how to approach combatting the disease.
Another new tree health resource is the UKPSF’s Ash Dieback web resource, which was launched this week. Mimi Tanimoto, Executive Officer of the UKPSF, said, “Speaking to scientists who wanted to do something to help combat ash dieback, I found a recurring problem that they were unsure of what else was happening. It was clear that by joining up the various projects we could better tackle the disease.” The website will be updated regularly with news, and it is possible to sign up on the site to receive these updates via email. Anyone who has news that they would like added to the site can contact Mimi at email@example.com.
The final piece of ash dieback news is that the Open Ash Dieback project, which crowdsources genome analysis of ash trees and the fungal pathogen Chalara fraxinea,published their first paper last week. Crowdsourcing genomic analyses of ash and ash dieback – power to the people by researchers from several UK universities, lead by two groups at the Sainsbury Laboratory, was published in GigaScience 2:2 doi:10.1186/2047-217X-2-2.